There has been a lot of speculation about this guitar. Clearly the neck pickup is the wrong way round, but that wouldn't cause the out of phase effect, but wiring it backwards would. I've simulated this with a second-hand Vintage V100 Les Paul copy I bought off eBay. The positioning of the volume controls is very important, bridge on about 8. neck on about 7 works for me. People who saw Peter in the early days said he would often make small adjustments to the volume controls during solos, bringing the out of phase sound in and out.
Most probably what happened with his guitar is that the magnet was replaced upside down so it's magnetically out of phase with the bridge pickup. He insists he didn't modify the guitar at all though, it was like that when he bought it.